Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SALL2

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293 cells
cell line
HEK293
genotype
KO
chip antibody
Sall2 (Bethyll)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell nuclei were sonicated to shear DNA in 300 μl of sonication buffer, using a Bioruptor Plus (Diagenode) (18 times, 15 sec on /20 sec off each time, 9 W potency), obtaining lengths between 300 and 600 bp. Immunoprecipitations were carried out overnight at 4 °C using 40 μg of chromatin and 5 μg of SALL2 (anti-SALL2; Bethyl). The SALL2 total knockout was used as a negative control of antibody binding To prepare each library was used the KAPA Hiper Prep kit and 7 adapters from the KAPA SI Adapters kit, both according to the manufacturer's protocols. Briefly, the first step in library preparation was to convert any overhangs in the ChIP DNA into phosphorylated blunt ends. The 3′ ends were then adenylated, and adaptors ligated onto the ends of the fragments. The library size (348 bp) and the DNA concentration (14,486 nM) was obtained by using an Agilent 2100 Bioanalyzer

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
14318780
Reads aligned (%)
83.5
Duplicates removed (%)
41.6
Number of peaks
342 (qval < 1E-05)

hg19

Number of total reads
14318780
Reads aligned (%)
82.9
Duplicates removed (%)
42.4
Number of peaks
267 (qval < 1E-05)

Base call quality data from DBCLS SRA